# Source code for MDAnalysis.selections.vmd

    # -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
    # vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
    #
    # MDAnalysis --- https://www.mdanalysis.org
    # Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
    # (see the file AUTHORS for the full list of names)
    #
    # Released under the Lesser GNU Public Licence, v2.1 or any higher version
    #
    # Please cite your use of MDAnalysis in published work:
    #
    # R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
    # D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
    # MDAnalysis: A Python package for the rapid analysis of molecular dynamics
    # simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
    # Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
    # doi: 10.25080/majora-629e541a-00e
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    # N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
    # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
    # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
    #

    """
    VMD selections
    ==============

    Write :class:`MDAnalysis.core.groups.AtomGroup` selection to a VMD_ `tcl` file
    (for example, "macros.vmd") that defines `atomselect macros`_. To be used in
    VMD like this (assuming the default macro name "mdanalysis001"):

    .. code-block:: tcl

       source macros.vmd
       set sel [atomselect top mdanalysis001]

    In the VMD_ GUI the macro "mdanalysis001" appears in the
    :menuselection:`Graphics --> Representations` window under
    :guilabel:`Selections: Singlewords`.

    .. _VMD: http://www.ks.uiuc.edu/Research/vmd/
    .. _atomselect macros: http://www.ks.uiuc.edu/Research/vmd/current/ug/node120.html

    .. autoclass:: SelectionWriter
       :inherited-members:

    """
    from . import base

    class SelectionWriter(base.SelectionWriterBase):
        format = "VMD"
        ext = "vmd"
        continuation = "\\"
        commentfmt = "# %s"

        def _write_head(self, out, **kwargs):
            out.write(self.comment("MDAnalysis VMD selection"))
            out.write("atomselect macro {name!s} {{index ".format(**kwargs))

        def _translate(self, atoms, **kwargs):
            # VMD index is 0-based (as is MDAnalysis)
            return [str(atom.index) for atom in atoms]

        def _write_tail(self, out, **kwargs):
            out.write("}")